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The way I was taught, you only rotate the brood chambers in the spring after the cluster has broken. Generally, the Queen will be in the top chamber and this will put her back down in the bottom to get started laying for that year. Once she has begun laying, she will travel up and down as needed to find open cells to lay in. You'll want to keep an eye out to see if the bees are filling the brood chambers completely with honey... this will be a sign to add supers. If they continue to fill the brood chambers, the Queen will lose laying cells and the overall population of the colony will suffer.

I use three deep brood chambers. I don't rotate boxes. I do reverse in the spring by putting the girls on the bottom. I use unlimited broodnest management that opens up the broodnest in the center of all three to keep the queen from hankering down.